Genetic Variant NM_003345.5:c.151-314G>A (chr16-1315340-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003345.5(UBE2I):c.151-314G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 400,680 control chromosomes in the GnomAD database, including 74,023 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.53 ( 23681 hom., cov: 34)

Exomes 𝑓: 0.63 ( 50342 hom. )

Consequence

UBE2I
NM_003345.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

Publications

8 publications found

Variant links:

Genes affected

UBE2I (HGNC:12485): (ubiquitin conjugating enzyme E2 I) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. Four alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

UBE2I links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2I	NM_003345.5 link	c.151-314G>A		intron_variant	Intron 3 of 6	ENST00000397514.8	NP_003336.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2I	ENST00000397514.8 link	c.151-314G>A		intron_variant	Intron 3 of 6	1	NM_003345.5	ENSP00000380649.3		P63279

Frequencies

GnomAD3 genomes

AF:

0.531

AC:

80750

AN:

151976

Hom.:

23685

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.632

Gnomad AMR

AF:

0.555

Gnomad ASJ

AF:

0.616

Gnomad EAS

AF:

0.902

Gnomad SAS

AF:

0.667

Gnomad FIN

AF:

0.678

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.613

Gnomad OTH

AF:

0.550

GnomAD4 exome

AF:

0.625

AC:

155406

AN:

248586

Hom.:

50342

Cov.:

AF XY:

0.627

AC XY:

82332

AN XY:

131228

show subpopulations

African (AFR)

AF:

0.278

AC:

2154

AN:

7752

American (AMR)

AF:

0.556

AC:

6513

AN:

11716

Ashkenazi Jewish (ASJ)

AF:

0.612

AC:

4366

AN:

7136

East Asian (EAS)

AF:

0.897

AC:

13178

AN:

14696

South Asian (SAS)

AF:

0.644

AC:

21923

AN:

34020

European-Finnish (FIN)

AF:

0.674

AC:

8517

AN:

12644

Middle Eastern (MID)

AF:

0.563

AC:

580

AN:

1030

European-Non Finnish (NFE)

AF:

0.616

AC:

89711

AN:

145676

Other (OTH)

AF:

0.608

AC:

8464

AN:

13916

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

2614

5228

7841

10455

13069

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

524

1048

1572

2096

2620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.531

AC:

80753

AN:

152094

Hom.:

23681

Cov.:

AF XY:

0.539

AC XY:

40070

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.278

AC:

11539

AN:

41490

American (AMR)

AF:

0.555

AC:

8491

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.616

AC:

2138

AN:

3470

East Asian (EAS)

AF:

0.902

AC:

4669

AN:

5178

South Asian (SAS)

AF:

0.667

AC:

3212

AN:

4816

European-Finnish (FIN)

AF:

0.678

AC:

7187

AN:

10602

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.613

AC:

41608

AN:

67914

Other (OTH)

AF:

0.553

AC:

1169

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1816

3632

5447

7263

9079

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

700

1400

2100

2800

3500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.549

Hom.:

3175

Bravo

AF:

0.511

Asia WGS

AF:

0.767

AC:

2666

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.59

(source)

DANN

Benign

0.40

PhyloP100

-1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over